Open Access Highly Accessed Methodology article

Next-generation sequencing for HLA typing of class I loci

Rachel L Erlich1, Xiaoming Jia12, Scott Anderson1, Eric Banks1, Xiaojiang Gao34, Mary Carrington34, Namrata Gupta1, Mark A DePristo1, Matthew R Henn1, Niall J Lennon1 and Paul IW de Bakker1567*

Author Affiliations

1 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

2 Harvard-MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA

3 Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick Inc., National Cancer Institute, Frederick, Maryland 21702, USA

4 Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts 02114, USA

5 Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA

6 Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands

7 Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands

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BMC Genomics 2011, 12:42  doi:10.1186/1471-2164-12-42

Published: 18 January 2011

Additional files

Additional file 1:

Sample preparation processes for HLA typing. Process map for (a) Library construction-based barcoding and (b) PCR-based barcoding.

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Additional file 2:

Data sequence characteristics generated from 270 HapMap individuals in three sample pools.

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Additional file 3:

Depth of Coverage Plate 1. Depth of coverage for 96 of 270 HapMap individuals sequenced on plate 1: (a) coverage by individual, and (b) coverage across each of 6 exons.

Format: PDF Size: 227KB Download file

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Additional file 4:

Depth of Coverage Plate 2. Depth of coverage for 96 of 270 HapMap individuals sequenced on plate 2: (a) coverage by individual, and (b) coverage across each of 6 exons.

Format: PDF Size: 222KB Download file

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Additional file 5:

Depth of Coverage Plate 3. Depth of coverage for 96 of 270 HapMap individuals sequenced on plate 3: (a) coverage by individual, and (b) coverage across each of 6 exons.

Format: PDF Size: 199KB Download file

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Additional file 6:

Sequence metrics generated in pilot study for the barcoded-PCR method in 95 HapMap individuals pooled on a single plate.

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Additional file 7:

Class I HLA types for 270 HapMap samples.

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Additional file 8:

Example of mistyping. IGV snapshot: an example of mistyping at HLA-A due to low 454 coverage of A*3001 (NA18507).

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Additional file 9:

Typing accuracy in 95 samples sequenced using the barcoded-PCR method.

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Additional file 10:

454 HLA Typing Methods and their Attributes.

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Additional file 11:

HLA class I primer sequences and locations.

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